% SYNCAT_TREE   ss. synaptic electrot. signature of elsyn-connected trees.
% (trees package)
%
% syn = syncat_tree (intrees, inodes1, inodes2, gelsyn, ge, gi, Ee, Ei, ...
%                    I, options) 
% -------------------------------------------------------------------------
%
% concatenates many trees with electrical synapses and calculates
% calculates the responses to synaptic input (see syn_tree). Indices are
% cumulative summing along trees; N is sum of all nodes in all trees.
%
% Input
% -----
% - intrees::cell array: cell array of trees
% - inodes1::array: indices for elsyn origin, indices are cumulated over trees
% - inodes2::array: indices of elsyn endpoints.
% - gelsyn::number or vector:conductance value or values if individual [uS]
% - ge::Nx1 vector or value:excitatory synaptic input ind. compartments
%       (or allround) {DEFAULT: 0 uS in all nodes}
% - gi::Nx1 vector or value:inhibitory synaptic input ind. compartments
%       (or allround) {DEFAULT: 0 uS in all nodes}
% - Ee::Nx1 vector or value:excitatory reversal potential ind. compartments
%       (or allround) {DEFAULT: 60 mV}
% - Ei::Nx1 vector or value:inhibitory reversal potential ind. compartments
%       (or allround) {DEFAULT: -20 mV}
% - I::Nx1 vector:current injection vector {DEFAULT 0 nA}
% - options::string: {DEFAULT: ''}
%     '-s' : show - full matrix if I is left empty (full sse)
%                 - tree distribution if I is Nx1 vector
%                 - other Is first column
%
% Output
% ------
% - syn::Nx1 matrix: voltage output
%
% Example
% -------
% be creative.. (see ssecat_tree)
%
% See also sse_tree syn_tree ssecat_tree M_tree loop_tree
% Uses M_tree ver_tree
%
% the TREES toolbox: edit, visualize and analyze neuronal trees
% Copyright (C) 2009  Hermann Cuntz

function syn = syncat_tree (intrees, inodes1, inodes2, gelsyn, ...
    ge, gi, Ee, Ei, I, options)

% trees : contains the tree structures in the trees package
global trees

if (nargin < 1)||isempty(intrees),
    intrees = trees;
end;

len = length (intrees);

for ward = 1 : len,
    ver_tree (intrees {ward});
end

siz = zeros (1, len);
for ward = 1 : len, 
    siz (ward) = length (intrees {ward}.X);
end;
sumsiz = [0 cumsum(siz)];
N = sumsiz (end);

if (nargin < 2)||isempty(inodes1),
    inodes1 = size (N, 1);
end

if (nargin < 3)||isempty(inodes2),
    inodes2 = 1;
end

if (nargin < 4)||isempty(gelsyn),
    gelsyn = 1;
end

if (nargin < 5)||isempty(ge),
    ge = sparse (N, 1);
end

if (nargin < 6)||isempty(gi),
    gi = sparse (N, 1);
end

if (nargin < 7)||isempty(Ee),
    Ee = 60;
end

if (nargin < 8)||isempty(Ei),
    Ei = -20;
end

if numel(ge)==1,
    dg = ge;
    ge = sparse (N, 1); ge (dg) = 1;
end

if numel(gi)==1,
    dg = gi;
    gi = sparse (N, 1); gi (dg) = 1;
end

if (nargin < 9)||isempty(I),
    I = sparse (size (N, 1), 1);
end

if (nargin < 10)||isempty(options),
    options = '';
end


MM = sparse (sumsiz (len + 1), sumsiz (len + 1));

for ward = 1 : len,
    MM (sumsiz (ward) + 1 : sumsiz (ward + 1), sumsiz (ward) + 1 : sumsiz (ward + 1)) = ...
        M_tree (intrees {ward});
end

if numel (gelsyn) == 1,
    gelsyn = ones (length (inodes1), 1) .* gelsyn;
end

for ward = 1 : length (inodes1),
    MM (inodes1 (ward), inodes2 (ward)) = MM (inodes1 (ward), inodes2 (ward)) - gelsyn (ward);
    MM (inodes2 (ward), inodes1 (ward)) = MM (inodes2 (ward), inodes1 (ward)) - gelsyn (ward);
    MM (inodes1 (ward), inodes1 (ward)) = MM (inodes1 (ward), inodes1 (ward)) + gelsyn (ward);
    MM (inodes2 (ward), inodes2 (ward)) = MM (inodes2 (ward), inodes2 (ward)) + gelsyn (ward);
end


% feed into M the synaptic conductances
MMg = MM + spdiags (ge, 0, N, N) + spdiags (gi, 0, N, N);
% and then inject the corresponding current
syn = MMg \ ((ge .* Ee) + (gi .* Ei) + I);

if strfind (options, '-s'),
    clf; hold on;
    X = zeros (N, 1); Y = zeros (N, 1); Z = zeros (N, 1);
    for ward = 1 : len,
        plot_tree (intrees {ward}, syn (sumsiz (ward) + 1 : sumsiz (ward + 1), 1));
        X (sumsiz (ward) + 1 : sumsiz (ward + 1)) = intrees {ward}.X;
        Y (sumsiz (ward) + 1 : sumsiz (ward + 1)) = intrees {ward}.Y;
        Z (sumsiz (ward) + 1 : sumsiz (ward + 1)) = intrees {ward}.Z;
    end;
    L   = [];
    ige = find (ge ~= 0);
    R   = rand (length (ige), 3) .* repmat ([50 50 150], length (ige), 1);
    HP  = line ([X(ige) X(ige) + R(:, 1)]',...
        [Y(ige) Y(ige) + R(:, 2)]',...
        [Z(ige) Z(ige) + R(:, 3)]');
    set (HP, 'linestyle', '-', 'color', [0 1 0], 'linewidth', 2);
    L (1) = HP (1);
    igi = find (gi ~= 0);
    R   = rand (length (igi), 3) .* repmat ([50 50 150], length (igi), 1);
    HP  = line ([X(igi) X(igi) + R(:, 1)]',...
        [Y(igi) Y(igi) + R(:, 2)]',...
        [Z(igi) Z(igi) + R(:, 3)]');
    set (HP, 'linestyle', '-', 'color', [1 0 0], 'linewidth', 2);
    L (2) = HP (1);
    L2  = line ([X(inodes1) X(inodes2)]', [Y(inodes1) Y(inodes2)]',...
        [Z(inodes1) Z(inodes2)]');
        set (L2, 'linestyle', '--', 'color', [0 0 0], 'linewidth', 2);
    L (3) = L2 (1);
    legend (L, {'exc', 'inh', 'elsyn'});
    colorbar;
    title ('potential distribution [mV]');
    xlabel ('x [\mum]'); ylabel ('y [\mum]'); zlabel ('z [\mum]');
    view(3); grid on; axis image;
end
